ABSTRACT Stratifying patients on the basis of molecular signatures could facilitate development of therapeutics that target pathways specific to a particular disease or tissue location. Previous studies suggest that pathogenesis of rheumatoid arthritis (RA) is similar in all affected joints. Here we show that distinct DNA methylation and transcriptome signatures not only discriminate RA fibroblast-like synoviocytes (FLS) from osteoarthritis FLS, but also distinguish RA FLS isolated from knees and hips. Using genome-wide methods, we discovered differences between RA knee and hip FLS in the methylation of genes encoding biological pathways, such as IL-6 signaling via JAK-STAT pathway. Furthermore, differentially expressed genes are identified between knee and hip FLS using RNA-seq. This proposal is designed to dissect joint-specific epigenetic and functional aspects of RA. To accomplish this, we will 1) develop a high resolution map of joint-specific and disease- specific DNA methylation patterns in RA including pathway analysis that integrates genomics and transcriptomics data; 2) determine the functional consequences of differential epigenetic marks by evaluating joint-specific FLS transcriptome patterns and cytokine responses; and 3) determine the mechanisms that define joint specific epigenetic marks, with a focus on the role of transcription factor motifs. These joint-specific epigenetic and functional signatures suggest that RA disease mechanisms might vary from joint to joint and potentially explain some of the diversity of drug responses in RA patients.